Update MNI-Colin27 #257
Update MNI-Colin27 #257
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UlrikeS91
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instances/latest/commonCoordinateSpaceVersions/MNI-Colin27/MNI-Colin27_1998.jsonld
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instances/latest/commonCoordinateSpaceVersions/MNI-Colin27/MNI-Colin27_1998.jsonld
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| "supportChannel": null, | ||
| "usedSpecimen": null, | ||
| "versionIdentifier": "2008", | ||
| "versionInnovation": "This is the high-resolution version of the common coordinate space. These volumes are defined at a 0.5 mm isotropic voxel grid in Talairach space, with dimensions 362x434x362 (XxYxZ) and start coordinates −90,−126,−72 (x,y,z)." |
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is dimension and start coordinates different between the versions?
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It's the summary provided by the developers. It was the least time-consuming solution and reflects what the developers want to highlight about this version. I added the sources, which hopefully make this more user-friendly.
instances/latest/commonCoordinateSpaceVersions/MNI-Colin27/MNI-Colin27_2008.jsonld
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| "usedSpecimen": null, | ||
| "versionIdentifier": "2008", | ||
| "versionInnovation": null | ||
| "axesOrigin": null, |
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Because it is not documented anywhere and wasn't filled out in this instance already (as opposed to 1998 version). I could probably figure it out somehow, but this will take a lot of time and effort.
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I will see if I get feedback on this from the MNI people
…-Colin27_1998.jsonld Co-authored-by: Lyuba Zehl <lyuba.zehl@ebrains.eu>
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I hope I can provide soon some more information for fixing some of the issues by talking to the MNI people.
| "defaultImage": null, | ||
| "description": "A stereotaxic average of T1-, T2- and PD-weighted MRI scans of the same individual (27, 12 and 12 scans, respectively). It was created at the Montreal Neurological Institute (MNI). The MRI scans were automatically registered to a common stereotaxic space using MRITOTAL (an automated volumetric registration procedure), resampled and intensity averaged. [sources: [Holmes et al. (1998)](https://doi.org/10.1097/00004728-199803000-00032) and descriptions provided under [‘MNI-Colin27’ on their homepage]( https://www.mcgill.ca/bic/software/tools-data-analysis/anatomical-mri/atlases)]", | ||
| "digitalIdentifier": null, | ||
| "fullDocumentation": { |
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I would kill this and use the link instead for the homepage
| }, | ||
| "fullName": "MNI Colin27 Average Brain Stereotaxic Registration Model", | ||
| "funding": null, | ||
| "homepage": "https://www.mcgill.ca/bic/software/tools-data-analysis/anatomical-mri/atlases", |
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replace with link from full documentation
| "fullName": "MNI Colin27 Average Brain Stereotaxic Registration Model", | ||
| "funding": null, | ||
| "homepage": "https://www.mcgill.ca/bic/software/tools-data-analysis/anatomical-mri/atlases", | ||
| "howToCite": "Please make sure to follow the copyright of the [MNI Colin27 Average Brain Stereotaxic Registration Model (original 1998 version)](https://www.mcgill.ca/bic/software/tools-data-analysis/anatomical-mri/atlases/colin-27). You may also cite its original publication, [Holmes et al. (1998)](http://doi.org/10.1097/00004728-199803000-00032).", |
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This is not the how to cite (unless you specifically found that as source from them)... The copyright notice should go specifically into the copyright (for now only holder and year in version 5.0 then also with the notice).
instances/latest/commonCoordinateSpaceVersions/MNI-Colin27/MNI-Colin27_1998.jsonld
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| "value": 67.0 | ||
| } | ||
| ], | ||
| "copyright": null, |
| "versionIdentifier": "2008", | ||
| "versionInnovation": null | ||
| "axesOrigin": null, | ||
| "copyright": null, |
| "fullName": "MNI Colin27 Average Brain Stereotaxic Registration Model", | ||
| "funding": null, | ||
| "homepage": "https://www.mcgill.ca/bic/software/tools-data-analysis/anatomical-mri/atlases", | ||
| "howToCite": "Please make sure to follow the copyright of the [MNI Colin27 Average Brain Stereotaxic Registration Model (high-resolution version 2008)](https://www.mcgill.ca/bic/software/tools-data-analysis/anatomical-mri/atlases/colin-27-2008). You may also cite its original publication, [Holmes et al. (1998)](http://doi.org/10.1097/00004728-199803000-00032), and the corresponding publication, [Aubert-Broche et al. (2006)](https://doi.org/10.1016/j.neuroimage.2006.03.052).", |
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see comment above. I'll try to clarify with the MNI people
| "supportChannel": null, | ||
| "usedSpecimen": null, | ||
| "versionIdentifier": "2008", | ||
| "versionInnovation": "This is the high-resolution version of the common coordinate space. These volumes are defined at a 0.5 mm isotropic voxel grid in Talairach space, with dimensions 362x434x362 (XxYxZ) and start coordinates −90,−126,−72 (x,y,z). [sources: [’Overview’ summary on their homepage]( https://www.mcgill.ca/bic/software/tools-data-analysis/anatomical-mri/atlases/colin-27-2008) and [Aubert-Broche et al. (2006)](https://doi.org/10.1016/j.neuroimage.2006.03.052)]" |
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To clarify: Talairach not used in original? what is meant with start coordinates ?
Start: This is a higher resolved variant of the original version...
| } | ||
| ], | ||
| "homepage": "https://www.mcgill.ca/bic/software/tools-data-analysis/anatomical-mri/atlases", | ||
| "howToCite": "Please make sure to follow the copyright of the [MNI Colin27 Average Brain Stereotaxic Registration Model](https://www.mcgill.ca/bic/software/tools-data-analysis/anatomical-mri/atlases/colin-27). You may also cite its original publication, [Holmes et al. (1998)](http://doi.org/10.1097/00004728-199803000-00032), and/or its later publication, [Aubert-Broche et al. (2006)](https://doi.org/10.1016/j.neuroimage.2006.03.052).", |
| "@id": "https://openminds.om-i.org/instances/commonCoordinateSpaceVersion/MNI-Colin27_2008" | ||
| } | ||
| ], | ||
| "homepage": "https://www.mcgill.ca/bic/software/tools-data-analysis/anatomical-mri/atlases", |
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kill this link (only keep homepages for the versions leading to the specific info pages of each version)
I tried to update the MNI-Colin27 CommonCoordinateSpace and its two versions. I had to change the description of the space since this describes how the original version was made. As far as I could tell, the newer version was made in a very similar way but resampled onto a 0.5 mm grid (and not a 1 mm grid as the original version). They also put a significantly larger focus on the T2- and PD-weighted scans (and the original version has average those as well, but focuses much less on it). Otherwise, I tried to add some more content to each but didn't change much about the existing content.
Let me know if I should change anything. I only made the changes in the 'latest' folder. I'll update the rest after a first review.